In the course of writing this book, answers to the following questions and many others were given in both narrative and visual form. Most of them were presented rather forcefully, and not when I was expecting them. I understood that I was to share what I learned. What is in store for the geology of North America? How do we create matter every day? What is the nature of nature? How did people live more than a half million years ago? (...) What was space travel like a half million years ago? Where is God? What are our responsibilities as humans? Is Hitler in heaven? How can we go to heaven? (shrink)

Philosophers of experiment have acknowledged that experiments are often more than mere hypothesis-tests, once thought to be an experiment's exclusive calling. Drawing on examples from contemporary biology, I make an additional amendment to our understanding of experiment by examining the way that `wide' instrumentation can, for reasons of efficiency, lead scientists away from traditional hypothesis-directed methods of experimentation and towards exploratory methods.

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...) arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

The interventionist account of causal explanation, in the version presented by Jim Woodward, has been recently claimed capable of buttressing the widely felt—though poorly understood—hunch that high-level, relatively abstract explanations, of the sort provided by sciences like biology, psychology and economics, are in some cases explanatorily optimal. It is the aim of this paper to show that this is mistaken. Due to a lack of effective constraints on the causal variables at the heart of the interventionist causal-explanatory scheme, as presently (...) formulated it is either unable to prefer high-level explanations to low, or systematically overshoots, recommending explanations at so high of a level as to be virtually vacuous. (shrink)

This paper critiques the new mechanistic explanatory program on grounds that, even when applied to the kinds of examples that it was originally designed to treat, it does not distinguish correct explanations from those that blunder. First, I offer a systematization of the explanatory account, one according to which explanations are mechanistic models that satisfy three desiderata: they must 1) represent causal relations, 2) describe the proper parts, and 3) depict the system at the right ‘level.’ Second, I argue that (...) even the most developed attempts to fulfill these desiderata fall short by failing to appropriately constrain explanatorily apt mechanistic models. -/- *This paper used to be called "The Emperor's New Mechanisms". (shrink)

Among the factors necessary for the occurrence of some event, which of these are selectively highlighted in its explanation and labeled as causes — and which are explanatorily omitted, or relegated to the status of background conditions? Following J. S. Mill, most have thought that only a pragmatic answer to this question was possible. In this paper I suggest we understand this ‘causal selection problem’ in causal-explanatory terms, and propose that explanatory trade-offs between abstraction and stability can provide a principled (...) solution to it. After sketching that solution, it is applied to a few biological examples, including to a debate concerning the ‘causal democracy’ of organismal development, with an anti-democratic (though not a gene-centric) moral. (shrink)

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...) or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life. (shrink)

The third edition gives particular attention to neuroimaging, which has emerged in the past decade as one of the most active areas of research in the field.

L. R. Reinhardt; III—Dualism and Categories, Proceedings of the Aristotelian Society, Volume 66, Issue 1, 1 June 1966, Pages 71–92, https://doi.org/10.1093/aris.

In computer science, an algorithm is an unambiguous specification of how to solve a class of problems. Algorithms can perform calculation, data processing and automated reasoning tasks. As an effective method, an algorithm can be expressed within a finite amount of space and time and in a well-defined formal language for calculating a function. Starting from an initial state and initial input (perhaps empty), the instructions describe a computation that, when executed, proceeds through a finite number of well-defined successive states, (...) eventually producing "output" and terminating at a final ending state. The transition from one state to the next is not necessarily deterministic; some algorithms, known as randomized algorithms, incorporate random input. This book introduces a set of concepts in solving problems computationally such as Growth of Functions; Backtracking; Divide and Conquer; Greedy Algorithms; Dynamic Programming; Elementary Graph Algorithms; Minimal Spanning Tree; Single-Source Shortest Paths; All Pairs Shortest Paths; Flow Networks; Polynomial Multiplication, to ways of solving NP-Complete Problems, supported with comprehensive, and detailed problems and solutions, making it an ideal resource to those studying computer science, computer engineering and information technology. (shrink)

Philosophical theories of explanation characterize the difference between correct and incorrect explanations. While remaining neutral as to which of these ‘first-order’ theories is right, this paper asks the ‘meta-explanatory’ question: is the difference between correct and incorrect explanation real, i.e., objective or mind-independent? After offering a framework for distinguishing realist from anti-realist views, I sketch three distinct paths to explanatory anti-realism.

The old ritual word macte was only vaguely understood even in Republican times. As is well known, the ancient critics connected the word with magis, magnus, and explained it as magis auctus. A glance at Walde's Wörterbuch reveals that many attempts have been made in modern times to solve the mystery; but the formidable equipment of the modern philologist has yielded little better results than the popular etymology of the ancients, the most favoured view to-day seeing in mactus the PPP (...) of a verb mago with macto as the frequentative which replaces it. The supposed semantic development of this verb, originally meaning ‘to increase’, has been set forth by Warde Fowler in a well-known passage, to which recent authorities have accorded their assent and praise: ‘the vitality of the deity … was really increased by placing on the altar the organs of life of the victim’. But this is a solution which ignores half the problem: macte and mactare are used not only of the deities but also of the victim. One can perhaps understand lovem mactare as ‘to magnify J.’, but not even by the most superficial analogy can we find a transition from here to the meaning typified in mactare vinum. Yet this is one of the most frequent usages of the word. So deep a gulf lies between the two semantic spheres of the verb that some scholars have sought to find in it two different verbs. But this is a counsel of despair which the editor of the Thesaurus dismisses with a non recte. We must agree, then, with Hey that the modern explanation is ‘sicher eine unrichtige’ and with Meillet-Ernout that there exists ‘aucune étymologie claire’. It is, therefore, surprising that so ill-founded a preconception should lead investigators to ignore or even dismiss important evidence which the ancient authorities offer for the solution of this problem. (shrink)

Whether any apology is possible for the form of this paper is doubtful; but perhaps a few words are allowable. The miscellaneous notes, of which it consists, are fairly well described by the title: at all events, the proposals contained in them—with, I fear, many others—have been pencilled at one time or another in one margin or another. Their age varies widely: two or three must go back to days when my only complete Euripides was Kirchhoff's editio minor and my (...) only Sophocles a copy of Tournier; the most date from middle age or ‘quidquid est illud inter iuvenem et senem medium in utriusque confinio positum’; but, whenever they were made, they were not made by a student of the Greek dramatists commanding the equipment that such a student ought to have. The equipment, in any case, was out of my reach; but, though I have read the plays often, I have read them only because the ancients have a way of enabling one to forget the moderns—as I was informed in my youth by an excellent scholar who has now forgotten both. I hope, therefore, that anyone who may happen to read the paper will overlook some errors and ignorances of the amateur; and, above all, if I may borrow a sentence from Markland's preface to his emendations on Lysias, ‘si quando dictatoria ista, Lege, vel Scribe, occurrent, scito me nihil aliud velle quam Forte legendum vel scribendum’. (shrink)

In a recent note Mr. T. B. Allen had corrected a reading of J. B. Cramer βρβειος ορ to προβτειος., but in a footnote he adds ‘When I made this correction I was not aware of the word πρβειος. Liddell and Scott and Sophocles share my ignorance. I found it in the Anecdota of Boissonade III 408: κ δ τν κρεν ρνιθας σθειν κα πρβεια κα περιστερς sim. 410, 412, 419. Boissonade quotes the word from a similar treatise by Hierophilus, (...) and the 1851 edition of Stephanus reproduces his note.’ This trisyllabic word πρβειος is obviously a ‘Reimbildung’ to ρνειος, μσχειος, ταρειος etc., and its occurrence clears up a papyrus reading which has long puzzled me. In P. Lond. 113, 10, 13 [VII] we read πρωβαων δερμτων, which Preisigke lists as ‘πρβαιος=προβτειος’ Until reading Allen's note I had supposed that the loss of the syllable -ατ- in προβτ-ειος, was a haplography induced by the following δερμ-τ-ων but there are now grounds for regarding the formation as genuine. Only the variation of the adjectival suffix -ειος × -αιος presents a difficulty. In clearing this up we shall be able to lay a number of ghost-words which have spooked in the second edition of Mayser's Grammatik der ptolemäischen Papyri. (shrink)